ComPrAn

[Petra-P]

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[bioc-issue-bot]

Hi @Petra-P

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: ComPrAn
Type: Package
Title: Complexome Profiling Analysis package
Version: 0.99.0
Authors@R: 
    c(person(given = "Rick",
 family = "Scavetta",
 role = c("aut"),
 email = "rick@scavetta.academy"),
      person(given = "Petra",
 family = "Palenikova",
 role = c("aut", "cre"),
 email = "pp451@cam.ac.uk",
 comment = c(ORCID = "0000-0002-2465-4370")))
Description: This package is for analysis of SILAC labeled complexome profiling
    data. It uses peptide table in tab-delimited format as an input and produces
    ready-to-use tables and plots.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: 
    data.table,
    dplyr,
    forcats,
    ggplot2,
    magrittr,
    purrr,
    tidyr,
    rlang,
    stringr,
    shiny,
    DT,
    RColorBrewer,
    VennDiagram,
    rio,
    scales,
    shinydashboard,
    shinyjs,
    stats,
    tibble,
    grid
RoxygenNote: 7.1.1
Suggests: 
    testthat (>= 2.1.0),
    knitr
VignetteBuilder: knitr
biocViews: MassSpectrometry, Proteomics, Visualization

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[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, skipped".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active
for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/ComPrAn to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: dafda3ab8d29db7408761282f395c66228326517

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details. This link will be active
for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/ComPrAn to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[hpages]

Hi @Petra-P ,

Thanks for submitting ComPrAn. Package looks good and is well documented but I noticed that some plots in the proteinWorkflow.html vignette are empty. The problematic plots are:

• In the "Co-migration plot of single protein group between label states" section:

• In the "Co-migration plot of two protein groups within label state" section:

Also the SILACcomplexomics.html vignette repeats these 2 sections and has the same problematic figures. Note that this kind of repetition in the documentation should be avoided ("Don't Repeat Yourself (DRY)" principle in software engineering which also applies to the documentation).

Thanks,
H.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: ef9e520c0f343b096a6d3e3c0b00a5a97ec7202f

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details. This link will be active
for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/ComPrAn to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[Petra-P]

Hi @hpages ,

Thank you very much for your comments. I edited the vignettes, removing the repeated part and replacing it with a link between SILACcomplexomics.html and proteinWorkflow.html.

I am not sure what might be causing the plots to show empty as I was not able to replicate the issue. After running
devtools::install_github("https://github.com/Scavetta/ComPrAn", build_vignettes = TRUE)
browseVignettes("ComPrAn")
I could see both plots in proteinWorkflow.html on Windows (R version 4.0.3 (2020-10-10); Platform: x86_64-w64-mingw32/x64 (64-bit); Running under: Windows 10 x64 (build 19041)) and Linux (R version 4.0.3 (2020-10-10); Platform: x86_64-pc-linux-gnu (64-bit); Running under: Ubuntu 20.04.1 LTS). Is there anything you would suggest to try to identify and solve the issue? Thank you!

[hpages]

Hi @Petra-P ,

It looks like you're using the wrong version of R. You're submitting a package for inclusion to BioC 3.13 which is based on R 4.1 (the current devel version of R) so you need to use that version to develop and test your package. After running:

library(devtools)
devtools::install_github("https://github.com/Scavetta/ComPrAn", build_vignettes=TRUE)
library(ComPrAn)
browseVignettes("ComPrAn")

my sessionInfo() is:

R Under development (unstable) (2021-02-05 r79941)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.10

Matrix products: default
BLAS:   /home/hpages/R/R-4.1.r79941/lib/libRblas.so
LAPACK: /home/hpages/R/R-4.1.r79941/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ComPrAn_0.99.2 devtools_2.3.2 usethis_2.0.1 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6           tidyr_1.1.2          prettyunits_1.1.1   
 [4] ps_1.5.0             assertthat_0.2.1     rprojroot_2.0.2     
 [7] digest_0.6.27        R6_2.5.0             cellranger_1.1.0    
[10] futile.options_1.0.1 ggplot2_3.3.3        pillar_1.4.7        
[13] rlang_0.4.10         curl_4.3             readxl_1.3.1        
[16] VennDiagram_1.6.20   rstudioapi_0.13      data.table_1.13.6   
[19] callr_3.5.1          DT_0.17              shinyjs_2.0.0       
[22] desc_1.2.0           stringr_1.4.0        foreign_0.8-81      
[25] htmlwidgets_1.5.3    munsell_0.5.0        compiler_4.1.0      
[28] pkgconfig_2.0.3      pkgbuild_1.2.0       htmltools_0.5.1.1   
[31] tidyselect_1.1.0     tibble_3.0.6         rio_0.5.16          
[34] crayon_1.4.1         dplyr_1.0.4          withr_2.4.1         
[37] later_1.1.0.1        grid_4.1.0           gtable_0.3.0        
[40] lifecycle_1.0.0      DBI_1.1.1            magrittr_2.0.1      
[43] formatR_1.7          scales_1.1.1         zip_2.1.1           
[46] cli_2.3.0            stringi_1.5.3        cachem_1.0.4        
[49] fs_1.5.0             promises_1.2.0.1     remotes_2.2.0       
[52] testthat_3.0.2       futile.logger_1.4.3  ellipsis_0.3.1      
[55] generics_0.1.0       vctrs_0.3.6          openxlsx_4.2.3      
[58] lambda.r_1.2.4       RColorBrewer_1.1-2   tools_4.1.0         
[61] forcats_0.5.1        glue_1.4.2           purrr_0.3.4         
[64] hms_1.0.0            processx_3.4.5       pkgload_1.1.0       
[67] fastmap_1.1.0        colorspace_2.0-0     sessioninfo_1.1.1   
[70] shinydashboard_0.7.1 memoise_2.0.0        haven_2.3.1         

Best,
H.

[LiNk-NY]

Hi @Petra-P @hpages

I've tested this on my computer and I can see the points
with Bioconductor 3.13.

Best,
Marcel

sessionInfo

> sessionInfo() R Under development (unstable) (2020-12-12 r79621) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.10

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] ComPrAn_0.99.2

loaded via a namespace (and not attached):
[1] zip_2.1.1 Rcpp_1.0.6 later_1.1.0.1
[4] cellranger_1.1.0 pillar_1.5.0 compiler_4.1.0
[7] formatR_1.7 RColorBrewer_1.1-2 futile.logger_1.4.3
[10] shinyjs_2.0.0 tools_4.1.0 forcats_0.5.1
[13] futile.options_1.0.1 digest_0.6.27 lifecycle_1.0.0
[16] tibble_3.1.0 gtable_0.3.0 debugme_1.1.0
[19] pkgconfig_2.0.3 rlang_0.4.10 openxlsx_4.2.3
[22] DBI_1.1.1 curl_4.3 VennDiagram_1.6.20
[25] haven_2.3.1 rio_0.5.26 stringr_1.4.0
[28] dplyr_1.0.4 hms_1.0.0 generics_0.1.0
[31] vctrs_0.3.6 htmlwidgets_1.5.3 shinydashboard_0.7.1
[34] grid_4.1.0 DT_0.17 tidyselect_1.1.0
[37] data.table_1.14.0 glue_1.4.2 R6_2.5.0
[40] fansi_0.4.2 readxl_1.3.1 foreign_0.8-81
[43] tidyr_1.1.3 purrr_0.3.4 ggplot2_3.3.3
[46] lambda.r_1.2.4 magrittr_2.0.1 promises_1.2.0.1
[49] scales_1.1.1 ellipsis_0.3.1 htmltools_0.5.1.1
[52] assertthat_0.2.1 colorspace_2.0-0 utf8_1.1.4
[55] stringi_1.5.3 munsell_0.5.0 crayon_1.4.1

[hpages]

Thanks @LiNk-NY for testing this. Really confusing that you can't reproduce this given that you're using the exact same OS as I do (Ubuntu 20.10).

BTW an easier way to reproduce (for me) is to just run the oneGroupTwoLabelsCoMigration example:

library(ComPrAn)
example(oneGroupTwoLabelsCoMigration)
# ...
# Hit <Return> to see next plot:

After hitting <Return> I get the following warning:

Warning message:
In grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page

and the following plot:

However, if I use alphaValue=1:

oneGroupTwoLabelsCoMigration(forAnalysis, max_frac, groupDV, groupName, alphaValue=1)

then everything is fine:

@Petra-P So maybe an easy workaround would be to just set alphaValue to 1 by default?

[LiNk-NY]

@hpaes I am able to output the plot.
Could it be differences in the R-devel version?
I am not sure what is causing this.

Here are my capabilities()

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE        TRUE        TRUE        TRUE        TRUE       FALSE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
        NLS       Rprof     profmem       cairo         ICU long.double 
       TRUE        TRUE       FALSE        TRUE        TRUE        TRUE 
    libcurl 
       TRUE 

[hpages]

Not sure either. I have the exact same capabilities().

FWIW I also tried with an older R-devel installation that I kept around (2020-11-18 r79449) and got the same thing (i.e. an empty plot). Maybe the semi-transparency capability of the X11 device is provided via an additional deb package? I'm starting to suspect a missing deb package in the X11 family.

This problem is real i.e. many users have reported the "semi-transparency is not supported on this device" problem. Until we understand what's going on exactly, let's avoid using alphaValue < 1.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 75eb33a4ee75a72b3e7dac0468d1d3fa40cafc80

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS".
This may mean there is a problem with the package that you need to fix.
Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active
for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/ComPrAn to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 5f8c1d8c4a17fb2a3311a3fbb885e5c00ca1f12b

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings
on all platforms.

Please see the build report for more details. This link will be active
for 21 days.

Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/ComPrAn to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[Petra-P]

Hi @hpages @LiNk-NY ,
Thank you for testing the package! I changed the default value of alphaValue to 1 in both functions to avoid the warning message for now. I also added a CITATION file as paper describing ComPrAn has been published recently (https://doi.org/10.1016/j.bbabio.2021.148399).

I am getting the semi-transparency waring message on Linux with R 4.1 (session info below). When using Rstudio I was able to display the plot correctly with alphaValue <1 after setting options(bitmapType="cairo").

On Windows with R 4.1 plot is displayed fine with alphaValue<1 (session info below).

Best,
Petra

Linux sessionInfo():

R Under development (unstable) (2021-02-20 r80030)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

atrix products: default
BLAS:   /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8
 [2] LC_NUMERIC=C
 [3] LC_TIME=sk_SK.UTF-8
 [4] LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=sk_SK.UTF-8
 [6] LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=sk_SK.UTF-8
 [8] LC_NAME=C
 [9] LC_ADDRESS=C
[10] LC_TELEPHONE=C
[11] LC_MEASUREMENT=sk_SK.UTF-8
[12] LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices
[4] utils     datasets  methods
[7] base

other attached packages:
[1] ComPrAn_0.99.2

loaded via a namespace (and not attached):
 [1] zip_2.1.1
 [2] Rcpp_1.0.6
 [3] later_1.1.0.1
 [4] cellranger_1.1.0
 [5] pillar_1.5.0
 [6] compiler_4.1.0
 [7] formatR_1.7
 [8] RColorBrewer_1.1-2
 [9] futile.logger_1.4.3
[10] shinyjs_2.0.0
[11] forcats_0.5.1
[12] futile.options_1.0.1
[13] tools_4.1.0
[14] digest_0.6.27
[15] lifecycle_1.0.0
[16] tibble_3.1.0
[17] gtable_0.3.0
[18] pkgconfig_2.0.3
[19] rlang_0.4.10
[20] openxlsx_4.2.3
[21] curl_4.3
[22] VennDiagram_1.6.20
[23] haven_2.3.1
[24] rio_0.5.16
[25] withr_2.4.1
[26] stringr_1.4.0
[27] dplyr_1.0.4
[28] hms_1.0.0
[29] generics_0.1.0
[30] vctrs_0.3.6
[31] htmlwidgets_1.5.3
[32] shinydashboard_0.7.1
[33] grid_4.1.0
[34] DT_0.17
[35] tidyselect_1.1.0
[36] glue_1.4.2
[37] data.table_1.14.0
[38] R6_2.5.0
[39] fansi_0.4.2
[40] readxl_1.3.1
[41] foreign_0.8-81
[42] farver_2.0.3
[43] tidyr_1.1.2
[44] purrr_0.3.4
[45] ggplot2_3.3.3
[46] lambda.r_1.2.4
[47] magrittr_2.0.1
[48] promises_1.2.0.1
[49] scales_1.1.1
[50] ellipsis_0.3.1
[51] htmltools_0.5.1.1
[52] colorspace_2.0-0
[53] utf8_1.1.4
[54] stringi_1.5.3
[55] munsell_0.5.0
[56] crayon_1.4.1

Windows sessionInfo():

R Under development (unstable) (2021-02-27 r80043)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=Slovak_Slovakia.1250  LC_CTYPE=Slovak_Slovakia.1250
[3] LC_MONETARY=Slovak_Slovakia.1250 LC_NUMERIC=C
[5] LC_TIME=Slovak_Slovakia.1250

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ComPrAn_0.99.4

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6           tidyr_1.1.3          prettyunits_1.1.1
 [4] ps_1.5.0             assertthat_0.2.1     rprojroot_2.0.2
 [7] digest_0.6.27        utf8_1.1.4           R6_2.5.0
[10] cellranger_1.1.0     futile.options_1.0.1 ggplot2_3.3.3
[13] pillar_1.5.1         rlang_0.4.10         curl_4.3
[16] readxl_1.3.1         VennDiagram_1.6.20   rstudioapi_0.13
[19] data.table_1.14.0    callr_3.5.1          DT_0.17
[22] shinyjs_2.0.0        desc_1.2.0           devtools_2.3.2
[25] stringr_1.4.0        foreign_0.8-81       htmlwidgets_1.5.3
[28] munsell_0.5.0        compiler_4.1.0       pkgconfig_2.0.3
[31] pkgbuild_1.2.0       htmltools_0.5.1.1    tidyselect_1.1.0
[34] tibble_3.1.0         rio_0.5.26           fansi_0.4.2
[37] later_1.1.0.1        crayon_1.4.1         dplyr_1.0.5
[40] withr_2.4.1          grid_4.1.0           gtable_0.3.0
[43] lifecycle_1.0.0      magrittr_2.0.1       formatR_1.7
[46] scales_1.1.1         zip_2.1.1            cli_2.3.1
[49] stringi_1.5.3        cachem_1.0.4         farver_2.1.0
[52] promises_1.2.0.1     fs_1.5.0             remotes_2.2.0
[55] testthat_3.0.2       futile.logger_1.4.3  ellipsis_0.3.1
[58] generics_0.1.0       vctrs_0.3.6          openxlsx_4.2.3
[61] lambda.r_1.2.4       RColorBrewer_1.1-2   tools_4.1.0
[64] forcats_0.5.1        glue_1.4.2           purrr_0.3.4
[67] hms_1.0.0            processx_3.4.5       pkgload_1.2.0
[70] fastmap_1.1.0        colorspace_2.0-0     sessioninfo_1.1.1
[73] shinydashboard_0.7.1 memoise_2.0.0        haven_2.3.1
[76] usethis_2.0.1

[hpages]

Thanks!

[bioc-issue-bot]

Your package has been accepted. It will be added to the
Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

[vjcitn]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

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(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("ComPrAn"). The package 'landing page' will be created at

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